The latest report shows not all children are receiving the recommended five doses of pertussis vaccine, but even among those who are, the effectiveness of the immunization wears off.

Researchers at the Centers for Disease Control and Protection (CDC) report in the Journal of the American Medical Association that while vaccines do work well in protecting against childhood infection with the pertussis bacterium, or whooping cough, that the strongest immunization occurred among kids in the year after their last shot than among those who finished their full immunization series more than five years ago.

This is the first-ever study to test the long-term effectiveness of current pertussis vaccines, which contain snippets of the pertussis bacterium and were introduced in the 1990s. The newer shots trigger fewer adverse reactions than previous versions, which contained whole pertussis bacterial cells, but public health officials had been concerned that the effectiveness of the shots weakened over time. The findings are significant in light of the major pertussis outbreaks in the U.S. over the past few years, which have caused illness in tens of thousands nationwide. Earlier this year, the CDC recommended that adults over age 19 also receive another dose of the older, whole cell pertussis vaccine to maintain immunity against the bacterium. Pertussis is highly contagious and sometimes fatal; symptoms including violent, uncontrollable coughing that can lead to breathing problems, pneumonia and convulsions.

For the new study, CDC researchers analyzed data from California’s major epidemic in 2010, the largest outbreak of the disease in that state for more than 60 years. Comparing 682 kids with confirmed or suspected pertussis to more than 2,000 healthy kids, researchers could conduct a thorough investigation of the vaccine’s effectiveness.

“We saw that there was high effectiveness for these vaccines in the short term and they continue to work well,” says CDC epidemiologist Lara Misegades, the lead study author. “They are our best tool for preventing pertussis.”

Overall, the study shows, kids with pertussis are eight times as likely to be unvaccinated as healthy kids. However, even some kids with a complete vaccination record still got sick, since no vaccine is 100% effective. The researchers estimate that during the first year following a child’s fifth and final pertussis shot, the vaccine effectiveness is 98%. Five years later, however, it drops to 71%.

“That means that five years after the last dose, around 71% of kids are protected against pertussis,” Misegades says.

But the remaining 29% are susceptible again. The CDC recommends that children get a final booster shot at age 11 or 12 to ensure adult immunity. Pregnant women and anyone who cares for small children should also get the shot, according to the CDC.

The fact that the immunity generated by the vaccine wears off over time isn’t surprising. But the drop-off associated with each year following pertussis vaccination is relatively large. CDC researchers were first tipped off to the dramatic decline, even before conducting the study, when disease monitoring data revealed an unusual age pattern among pertussis cases nationwide.

Typically, pertussis hits infants hardest and then incidence drops off among older kids, who have stronger immune systems and start to benefit from being immunized. But in recent pertussis outbreaks, while incidence is still highest among infants (all of the deaths in California‘s 2010 epidemic were among babies) with lower rates among toddlers and pre-schoolers, incidence has been unexpectedly high among kids aged seven to ten. The CDC researchers interpreted that trend as a sign that vaccine protection might be wearing off over time.

But since the latest pertussis vaccines are so new, no one had studied the question of waning immunity. The older vaccines contained inactivated whole cells of pertussis bacteria, and effectively protected against infection but caused soreness and swelling at the injection site. According to the CDC’s Stacey Martin, a co-author on the new study, there were also concerns about possible neurological side effects, although those were never confirmed. In 1997, a new acellular vaccine, called DTaP, was recommended for all five childhood doses of the pertussis immunization series, which are given at 2, 4, 6, and 18 months and when children are four to six years old. The first group of children who received a full series of those shots are finally old enough to examine for disease outcomes.

The results suggest that in order to improve protection against pertussis, health officials may need to change the timing of vaccine doses. But while the authors say they have shared their findings with the CDC’s Advisory Committee on Immunization Practices, which draws up national guidelines they recognize that changing the schedule may not be easy.

“There’s very little room in the current [immunization] schedule to move doses around,” says Misegades. Doses are arranged to take advantage of both the optimum time to build up children’s immunity as well as exploit times when children go to doctors for health checkups, typically before starting school. “The fifth dose of the series is usually timed with school entry.” Likewise, she adds, the adolescent booster shot at age 11 or 12 is usually timed to coincide with a general health check-up at that time. Misegades says she worries that moving vaccine doses around, and out of sync with other medical services, may inadvertently cause kids to miss some shots altogether, leading to worse vaccine coverage.

Instead of altering the vaccination schedule, Misegades hopes more effective shots will address the problem of waning immunity. “Ideally we would like to have vaccines that are as safe as the current vaccines, but provide longer duration of protection,” she says.